New class of gene-termini-associated human RNAs suggests a novel RNA copying mechanism (original) (raw)

Nature volume 466, pages 642–646 (2010)Cite this article

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Abstract

Small (<200 nucleotide) RNA (sRNA) profiling of human cells using various technologies demonstrates unexpected complexity of sRNAs with hundreds of thousands of sRNA species present1,2,3,4. Genetic and in vitro studies show that these RNAs are not merely degradation products of longer transcripts but could indeed have a function1,2,5. Furthermore, profiling of RNAs, including the sRNAs, can reveal not only novel transcripts, but also make clear predictions about the existence and properties of novel biochemical pathways operating in a cell. For example, sRNA profiling in human cells indicated the existence of an unknown capping mechanism operating on cleaved RNA2, a biochemical component of which was later identified6. Here we show that human cells contain a novel type of sRNA that has non-genomically encoded 5′ poly(U) tails. The presence of these RNAs at the termini of genes, specifically at the very 3′ ends of known mRNAs, strongly argues for the presence of a yet uncharacterized endogenous biochemical pathway in cells that can copy RNA. We show that this pathway can operate on multiple genes, with specific enrichment towards transcript-encoding components of the translational machinery. Finally, we show that genes are also flanked by sense, 3′ polyadenylated sRNAs that are likely to be capped.

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Data deposits

Sequencing datasets described in this study have been deposited at the National Center for Biotechnology Information (NCBI) Short Read Archive (SRA), accession no SRA012676.

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Acknowledgements

We wish to thank A. Willingham, J. Thompson and Z. Li for discussions and help in the preparation of the manuscript. S.E.A. is supported by the Swiss National Science Foundation, B.J. by the NIH (GM079756) and American Cancer Society (RSG0905401), and A.P.M. by the NIH (MH60774). S.F. acknowledges support by a grant from the Comunidad de Madrid and European Union (Exp. 11/2009).

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Author notes

  1. Philipp Kapranov, Fatih Ozsolak, Sang Woo Kim and Sylvain Foissac: These authors contributed equally to this work.

Authors and Affiliations

  1. Helicos BioSciences Corporation, 1 Kendall Sq. Ste B7301 Cambridge, Massachusetts 02139-1671, USA ,
    Philipp Kapranov, Fatih Ozsolak, Doron Lipson, Chris Hart, Steve Roels & Patrice M. Milos
  2. Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, 15260, Pennsylvania, USA
    Sang Woo Kim & Bino John
  3. Integromics, S.L., Grisolía 2, 28760 Tres Cantos, Madrid, Spain ,
    Sylvain Foissac
  4. Department of Genetic Medicine and Development, University of Geneva Medical School, University of Geneva, 1 rue Michel-Servet, 1211 Geneva, Switzerland,
    Christelle Borel & Stylianos E. Antonarakis
  5. Department of Neurobiology, University of Pittsburgh, 3501 Fifth Avenue, Pittsburgh, 15260, Pennsylvania, USA
    A. Paula Monaghan

Authors

  1. Philipp Kapranov
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  2. Fatih Ozsolak
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  3. Sang Woo Kim
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  4. Sylvain Foissac
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  5. Doron Lipson
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  6. Chris Hart
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  7. Steve Roels
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  8. Christelle Borel
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  9. Stylianos E. Antonarakis
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  10. A. Paula Monaghan
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  11. Bino John
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  12. Patrice M. Milos
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Contributions

P.K., F.O. and P.M.M. designed the study, performed the experiments and the data analysis. S.F. and D.L. performed additional bioinformatics analyses. C.H. and S.R. assisted with the development of the Helicos analysis pipeline. S.W.K., A.P.M. and B.J. performed the northern blot and RPA validation experiments. C.B. and S.E.A. contributed to the validation experiments.

Corresponding authors

Correspondence toPhilipp Kapranov or Patrice M. Milos.

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Competing interests

P.K., F.O., D.L., C.H. and P.M.M. are employees and stockholders of Helicos BioSciences Corporation. S.F. is an employee of Integromics, S.L.

Supplementary information

Supplementary Information

This file contains Supplementary Text, Supplementary Methods and Materials, References, Supplementary Tables S1 –S2, Supplementary Figures S1-S8 and Supplementary Data for Human Expressed Sequence Tags. (PDF 2599 kb)

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Kapranov, P., Ozsolak, F., Kim, S. et al. New class of gene-termini-associated human RNAs suggests a novel RNA copying mechanism.Nature 466, 642–646 (2010). https://doi.org/10.1038/nature09190

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Editorial Summary

Another clutch of small RNAs

An analysis of short RNAs (with fewer than 200 nucleotides) from human cells using single molecule high-throughput sequencing has uncovered a previously unknown short RNA species with a difference. They all have the same 'tail' at their 5' ends, consisting of a sequence of non-genomically encoded polyU residues. This, together with the finding that these RNAs are closely associated with the 3' ends of known RNAs, points to the existence of a novel RNA-copying mechanism in human cells.